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2iyp

product rup

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING

LACTOCOCCUS LACTIS

UniProt P96789

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 RIBULOSE-5-PHOSPHATE × 1 ADENOSINE-2'-5'-DIPHOSPHATE × 1 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 ADENOSINE-2'-5'-DIPHOSPHATE × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
2iyo 2iyp 2iyp 2iz0 2iz0 2iz1 2iz1

7 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name 6PGD_LACLC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–473； UniProt 1–472 Author chain B； PDBConstruct 2–473； UniProt 1–472 Author chain C； PDBConstruct 2–473； UniProt 1–472

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id2iyp
Deposition date deposition_date2006-07-21
Structure title titleproduct rup
Keywords keywordsOXIDOREDUCTASE, 6-PHOSPHOGLUCONATE DEHYDROGENASE, NADP, PENTOSE SHUNT, GLUCONATE UTILIZATION; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2iyp__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2iyp__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2iyp__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）30.62 Å
Rg (electron density)29.74 Å
Total Rg30.48 Å
Atom count7441
Residues941
Excluded volume132280 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2iyp__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2iyp__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd2iypa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.0 — automated matches
Domain ID domain_idd2iypa2
Class classa — All alpha proteins
Fold Fold folda.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily Superfamily superfamilya.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Family Family familya.100.1.0 — automated matches
Domain ID domain_idd2iypb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.0 — automated matches
Domain ID domain_idd2iypb2
Class classa — All alpha proteins
Fold Fold folda.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily Superfamily superfamilya.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Family Family familya.100.1.0 — automated matches
Domain ID domain_idd2iypc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.0 — automated matches
Domain ID domain_idd2iypc2
Class classa — All alpha proteins
Fold Fold folda.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily Superfamily superfamilya.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Family Family familya.100.1.0 — automated matches

CATH v4.4 (9 domains)

Domain ID domain_id2iypA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2iypA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Homologous superfamily homologous superfamily10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Domain ID domain_id2iypA03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily320 — 6-Phosphogluconate Dehydrogenase, domain 3
Domain ID domain_id2iypB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2iypB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Homologous superfamily homologous superfamily10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Domain ID domain_id2iypB03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily320 — 6-Phosphogluconate Dehydrogenase, domain 3
Domain ID domain_id2iypC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2iypC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Homologous superfamily homologous superfamily10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Domain ID domain_id2iypC03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily320 — 6-Phosphogluconate Dehydrogenase, domain 3
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7. Citations (1)